Phylogenetic Analysis, Gene Structure Prediction and Conserved Motif Identification

Multiple sequence alignment was performed using Clustal X version 2.0 program (Larkin et al., 2007) with default parameters. Subsequently, MEGA version 5.0 software (Tamura et al., 2011) were employed to construct an unrooted phylogenetic tree, using the method of Neighbor Joining with pairwise deletion option, poisson correction model and uniform rates (rates among sites). Bootstrap tests with 1000 replicates were carried out to evaluate the statistical reliability of phylogenetic tree. The gene structure of BCCP genes were obtained through comparing the genomic sequences and their predicted coding sequences using the Gene Structure Display Server (GSDS) tool¹⁰ (Hu et al., 2015). BCCP protein sequences in G. arboreum, G. raimondii, G. hirsutum, and G. barbadense were submitted to online MEME program¹¹ (Bailey et al., 2009) for identification of conserved protein motifs. The MEME parameters were as follows: any number of repetitions, maximum number of motifs: 4, and optimum motif widths from 6 to 80 AA residues.